Post-unblinding augmentation trial data

Author

Laura Symul, Laura Vermeren

Published

January 9, 2026

Code
library(tidyverse)
library(magrittr)
library(gt)
library(patchwork)
library(SummarizedExperiment)
library(tidySummarizedExperiment)
library(MultiAssayExperiment)

tmp <- fs::dir_map("R scripts/", source)
tmp <- fs::dir_map("../VIBRANT-99-utils/R/", source)
rm(tmp)
theme_set(theme_light())

The purpose of this document is to compute additional “calculated variables” that require unblinded data, and to save the updated MultiAssayExperiment object for downstream analyses.

Loading the MultiAssayExperiment object

Code
mae_files <- 
  fs::dir_ls(
    get_04_output_dir(),
    regexp = "mae_full_.*\\.rds$"
  ) |> 
  sort(decreasing = TRUE) |>
  magrittr::extract(1)

mae <- readRDS(mae_files)

rm(mae_files)

Calculated variables

Saving the MultiAssayExperiment objects

The unblinded and augmented MAE object is saved to disk as an .rds file that can be loaded for downstream analyses.

Code
saveRDS(
  mae, 
  str_c(
    get_05_output_dir(),  
    "mae_full_", today() |> str_remove_all("-"), ".rds"
  )
)